Dr. Luigi is a falling block game using the same base mechanics as Dr. Mario. The player must pile-up colored pill-shaped blocks to clear the game matrix of the blue, red and yellow viruses. In this game, however, the pills come in pair, shaped like a 'L'. When four blocks and viruses of the same color align, they disappear, allowing various combos. The goal is to clear the matrix before the blocks reach the top and Dr. Luigi can't add any more pills. This game mode is called 'Operation L', but for the nostalgic players who prefer the classic Dr. Mario mode, the Retro Remedy Mode is also available. The goal stays the same, but single two-block pills fall instead of L-shaped ones.

The player can move and turn the blocks either using the gamepad buttons, or use the gamepad's touch-screen and a stylus. The game includes a versus mode to play against other players online or locally, or against AI.